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The two subspecies of Atlantic bay scallop ( Argopecten irradians ),  A. i. irradians  and  A. i. concentricus , are economically important aquacultural species in northern and southern China. Here, we performed the whole-genome sequencing, assembly, and gene annotation and produced draft genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of raw reads were generated from Illumina Hiseq and PacBio platforms for  A. i. irradians  and  A. i. concentricus , respectively. Draft genomes of 835.7 Mb and 874.82 Mb were assembled for the two subspecies, accounting for 83.9% and 89.79% of the estimated sizes of their corresponding genomes, respectively. The contig N50 and scaffold N50 were 78.54 kb and 1.53 Mb for the  A. i. irradians  genome, and those for the  A. i. concentricus  genome were 63.73 kb and 1.25 Mb. Moreover, 26,777 and 25,979 protein-coding genes were predicted for  A. i. irradians  and  A. i. concentricus , respectively. These valuable genome assemblies lay a solid foundation for future theoretical studies and provide guidance for practical scallop breeding.

Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus